Alignments for a candidate for trpD_2 in Desulfovibrio oxyclinae DSM 11498

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Desulfovibrio oxyclinae DSM 11498

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate WP_018123677.1 B149_RS0102980 anthranilate phosphoribosyltransferase

Query= curated2:C6C1D5
         (329 letters)



>NCBI__GCF_000375485.1:WP_018123677.1
          Length = 336

 Score =  336 bits (862), Expect = 4e-97
 Identities = 170/321 (52%), Positives = 226/321 (70%), Gaps = 4/321 (1%)

Query: 9   LTALSSGQDLTTEQADAVFEELFSGEMTNAQAGALLMGLRTKGEKAVEVAAGVRAALREA 68
           L  L+ G+ LT EQA A+F+ L +G++  AQAGA LMGLR KGE + ++AAGVRA L  A
Sbjct: 8   LDTLAKGESLTDEQASAMFDRLMNGDLHPAQAGAFLMGLRAKGEDSTDIAAGVRAGLDRA 67

Query: 69  KLIKGINSP----CIDTCGTGGDGTNSFNCSTAVAIYLADMGYLVTKHGNRAVSSSCGSA 124
             I G + P     IDTCGTGGDG+ SFNCSTA A++LADMG+ V KHGNRA+SSSCGSA
Sbjct: 68  LKIPGYDGPNGKPVIDTCGTGGDGSMSFNCSTATALFLADMGHCVAKHGNRALSSSCGSA 127

Query: 125 DVLEDLGVSLGTTVNEARDVLLRDKFVFMFAPNYHPAFGKIAPIRKELGIPTLFNLMGPL 184
           D LED+GV +  T  EA   L    F F+FAP YHPAF  + PIR+ LGI T+FN MGPL
Sbjct: 128 DALEDIGVPIENTPEEAAKQLDAANFTFLFAPAYHPAFKHVMPIRQALGIRTVFNFMGPL 187

Query: 185 LNPARPTHQILGVGRPEILRLMAEVLVLTNVEKAYVIHGAGNFDELTPFGVNDAILVENG 244
           LNPARP+HQ++GVG PE L++M E L+LT V++A+VI G G FDE+T FG      + +G
Sbjct: 188 LNPARPSHQLMGVGDPERLQIMGESLLLTGVDRAFVISGTGGFDEVTTFGPARGYFIHDG 247

Query: 245 ELTEVKIDPADYGFAAAKPEDVAVKDRPEALATIRKVLAGTAPQAMLDMVALNLGAAISI 304
            + +  I+P   GF A  P+DV V+DR +A+A +R++L G  P+AM+DMVA+NL A +++
Sbjct: 248 IMEKTTINPDRMGFKAHSPDDVRVQDRAQAVAVLREILDGNGPRAMMDMVAVNLAACLNL 307

Query: 305 LDGVSLEEGMEKAKAKVAKGV 325
           L   ++ E  + A+ KV +G+
Sbjct: 308 LGEGTMRECADIARDKVNEGL 328


Lambda     K      H
   0.316    0.134    0.375 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 309
Number of extensions: 9
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 329
Length of database: 336
Length adjustment: 28
Effective length of query: 301
Effective length of database: 308
Effective search space:    92708
Effective search space used:    92708
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_018123677.1 B149_RS0102980 (anthranilate phosphoribosyltransferase)
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01245.hmm
# target sequence database:        /tmp/gapView.20591.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01245  [M=330]
Accession:   TIGR01245
Description: trpD: anthranilate phosphoribosyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-100  321.9   0.0   3.1e-100  321.6   0.0    1.0  1  lcl|NCBI__GCF_000375485.1:WP_018123677.1  B149_RS0102980 anthranilate phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000375485.1:WP_018123677.1  B149_RS0102980 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.6   0.0  3.1e-100  3.1e-100       2     318 ..       9     327 ..       8     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 321.6 bits;  conditional E-value: 3.1e-100
                                 TIGR01245   2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke...e 67 
                                                +l+++++L++e+a ++++ +m+g++++aq +A+l+ lr+kge+  +ia+ ++a +++a k++     +
  lcl|NCBI__GCF_000375485.1:WP_018123677.1   9 DTLAKGESLTDEQASAMFDRLMNGDLHPAQAGAFLMGLRAKGEDSTDIAAGVRAGLDRALKIPGYdgpN 77 
                                               678999*******************************************************99764557 PP

                                 TIGR01245  68 seelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvar 136
                                                + ++D++GTGGDg+ ++N STa+al +a +G  vaKhGnr+ ss++GsaD Le +gv +e++pe++a+
  lcl|NCBI__GCF_000375485.1:WP_018123677.1  78 GKPVIDTCGTGGDGSMSFNCSTATALFLADMGHCVAKHGNRALSSSCGSADALEDIGVPIENTPEEAAK 146
                                               899****************************************************************** PP

                                 TIGR01245 137 sleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlkn 205
                                               +l+  +++FlfAP+yhpa+k+v+p+R+ Lg+rtvfN++GPLlnPar+++q++Gv +++ ++++ e l  
  lcl|NCBI__GCF_000375485.1:WP_018123677.1 147 QLDAANFTFLFAPAYHPAFKHVMPIRQALGIRTVFNFMGPLLNPARPSHQLMGVGDPERLQIMGESLLL 215
                                               ********************************************************************* PP

                                 TIGR01245 206 lgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkev 274
                                                gv+ra+v++g +g DE++++g+++ + ++dg +e++t++p  +g+k ++ +++++++ ++ +++l+e+
  lcl|NCBI__GCF_000375485.1:WP_018123677.1 216 TGVDRAFVISGTGGFDEVTTFGPARGYFIHDGIMEKTTINPDRMGFKAHSPDDVRVQDRAQAVAVLREI 284
                                               ********************************************************************* PP

                                 TIGR01245 275 legkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksg 318
                                               l g++ +a  d+v++N aa l + g+  +++e ++ a++++++g
  lcl|NCBI__GCF_000375485.1:WP_018123677.1 285 LDGNGPRAMMDMVAVNLAACLNLLGEG-TMRECADIARDKVNEG 327
                                               ***********************9987.9*********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (336 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.78
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis